How can I clean a PDB file using VMD or NAMD?

Question

[user366312]

I have 3884 PDB files generated by pd2_ca2main.

All of these files have duplicate atoms or alternate coordinates.

How can I clean these PDB files using VMD or NAMD?

Can anyone tell me what command I should use in console mode?

[Mensur Dlakic]

These programs are not meant for PDB cleaning. They use PDB files as a starting point for simulations, and can also visualize PDB contents.

Don't know exactly what the problem is with your files, but I can state with certainty that it is not unique to you. That plus the fact PDB files have been around for 40+ years means someone has solved it. I would start from pd2_ca2main and search for scripts that clean up files after it, or go with scripts that pre-process files as input to VMD/NAMD.

[user366312]

https://www.researchgate.net/post/How_to_Remove_different_version_of_atom_from_pdb_Crystal_Structure_for_Docking_Preparation/6022a146eebce870dc6df51a/citation/download

This link says that VMD can be used to clean PDB files.

It talks about other tools, too. However, I am very novice at using them.

[Mensur Dlakic]

The link says that PDB plugin for VMD, not VMD, can be used to clean PDB files. It also gives a bunch of secondary links to other tools, so it is up to you to pick one.